The goal of scib (single-cell integration and benchmarking) is to provide a unified way to perform data integration and benchmarking when the ground truth is available.
| method* | Package for wrapper | Publication | DOI |
|---|---|---|---|
| CCA | Seurat | Stuart T. et al. Cell (2019) | https://doi.org/10.1016/j.cell.2019.05.031 |
| RPCA | Seurat | Stuart T. et al. Cell (2019) | https://doi.org/10.1016/j.cell.2019.05.031 |
| Harmony | Seurat | Korsunsky, I. et al. Nat Methods (2019) | https://doi.org/10.1038/s41592-019-0619-0 |
| FastMNN | SeuratWrapper | Haghverdi, L. et al. Nat. Biotechnol. (2018) | https://doi.org/10.1038/s41421-019-0114-x |
| SCVI | SeuratWrapper | Lopez, R.et al. Nat Methods (2018) | https://doi.org/10.1038/s41592-018-0229-2 |
| BBKNN | scib (this package) | Krzysztof Polański et al. Bioinformatics (2020) | https://doi.org/10.1093/bioinformatics/btz625 |
| CONOS | scib (this package) | Barkas, N et al. Nat Methods (2019) | https://doi.org/10.1038/s41592-019-0466-z |
| LIGER | scib (this package) | Liu, J.et al. Nat. Protocols (2020) | https://doi.org/10.1038/s41596-020-0391-8 |
| SCANORAMA | scib (this package) | Hie, B et al. Nat Biotechnology (2019) | https://doi.org/10.1038/s41587-019-0113-3 |
| SCMC | scib (this package) | Zhang, L. et al. Genome Biology (2021) | https://doi.org/10.1186/s13059-020-02238-2 |
* The specific method can be called by appending the word "Integration" to the method name (e.g. HarmonyIntegration) for IntegrateLayers2() in scib package.
Installation of scib and dependencies
Example of running and evaluating one data integration method
Example of running and evaluating multiple data integration methods